iMOWSE, a scoring scheme bridging in silico and in vitro digestion in peptide mass fingerprints

Author(s):  
Stephen Kwok-Wing Tsui ◽  
Ka-Kit Leung
2021 ◽  
Vol 99 (2) ◽  
Author(s):  
Walter J J Gerrits ◽  
Marijke T A Schop ◽  
Sonja de Vries ◽  
Jan Dijkstra

Abstract Growing importance of upcycling agricultural by-products, food waste, and food processing by-products through livestock production strongly increased the variation in the nutritional quality of feed ingredients. Traditionally, feed ingredients are evaluated based on their measured extent of digestion. Awareness increases that in addition to the extent, the kinetics of digestion affects the metabolic fate of nutrients after absorption. Together with a growing body of evidence of complex interactions occurring within the lumen of the digestive tract, this urges the need of developing new approaches for feed evaluation. In a recently developed approach, we propose combining in vitro and in silico methods for feed ingredient evaluation. First steps in the development of such a systems were made by (1) evaluating in vitro the digestion potential of feed ingredients, regarding this as true ingredient properties and (2) predicting in silico the digestive processes like digesta transit, nutrient hydrolysis and absorption using dynamic, mechanistic modeling. This approach allows to evaluate to what extent the digestion potential of each ingredient is exploited in the digestive tract. Future efforts should focus on modeling digesta physicochemical properties and transit, applying in vitro digestion kinetic data of feed ingredients in mechanistic models, and generating reliable in vivo data on nutrient absorption kinetics across feed ingredients. The dynamic modeling approach is illustrated by a description of a modeling exercise that can be used for teaching purposes in digestive physiology or animal nutrition courses. A complete set of equations is provided as an on-line supplement, and can be built in modeling software that is freely available. Alternatively, the model can be constructed using any modeling software that enables the use of numerical integration methods.


Author(s):  
Markus Boel ◽  
Oscar J. Abilez ◽  
Ahmed N Assar ◽  
Christopher K. Zarins ◽  
Ellen Kuhl

Author(s):  
Jaynthy C. ◽  
N. Premjanu ◽  
Abhinav Srivastava

Cancer is a major disease with millions of patients diagnosed each year with high mortality around the world. Various studies are still going on to study the further mechanisms and pathways of the cancer cell proliferation. Fucosylation is one of the most important oligosaccharide modifications involved in cancer and inflammation. In cancer development increased core fucosylation by FUT8 play an important role in cell proliferation. Down regulation of FUT8 expression may help cure lung cancer. Therefore the computational study based on the down regulation mechanism of FUT8 was mechanised. Sapota fruit extract, containing 4-Ogalloylchlorogenic acid was used as the inhibitor against FUT-8 as target and docking was performed using in-silico tool, Accelrys Discovery Studio. There were several conformations of the docked result, and conformation 1 showed 80% dock score between the ligand and the target. Further the amino acids of the inhibitor involved in docking were studied using another tool, Ligplot. Thus, in-silico analysis based on drug designing parameters shows that the fruit extract can be studied further using in-vitro techniques to know its pharmacokinetics.


2019 ◽  
Author(s):  
Filip Fratev ◽  
Denisse A. Gutierrez ◽  
Renato J. Aguilera ◽  
suman sirimulla

AKT1 is emerging as a useful target for treating cancer. Herein, we discovered a new set of ligands that inhibit the AKT1, as shown by in vitro binding and cell line studies, using a newly designed virtual screening protocol that combines structure-based pharmacophore and docking screens. Taking together with the biological data, the combination of structure based pharamcophore and docking methods demonstrated reasonable success rate in identifying new inhibitors (60-70%) proving the success of aforementioned approach. A detail analysis of the ligand-protein interactions was performed explaining observed activities.<br>


2013 ◽  
Vol 999 (999) ◽  
pp. 1-15
Author(s):  
H.K. Ho ◽  
G. Nemeth ◽  
Y.R. Ng ◽  
E. Pang ◽  
C. Szantai-Kis ◽  
...  

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